[1] "Preparing Project:"
[1] "Hereeeeee"
[1] "Creating Object from..."
[1] "Patient data:"
[1] FALSE
[1] "Reading expression:tcga_coad_cms4.rds"
class: RangedSummarizedExperiment 
dim: 63856 115 
metadata(8): time_created recount3_version ... annotation recount3_url
assays(1): raw_counts
rownames(63856): ENSG00000278704.1 ENSG00000277400.1 ...
  ENSG00000182484.15_PAR_Y ENSG00000227159.8_PAR_Y
rowData names(10): source type ... havana_gene tag
colnames(115): 70969845-95d5-4324-ae22-8d8cd725021d
  c25b7166-f8af-44f2-ae53-e837971dbf37 ...
  5729d32f-0e42-46a5-b301-5ed3cc7aa2db
  623c5f2d-0489-4b20-abda-9d726cacaff2
colData names(937): rail_id external_id ... recount_seq_qc.errq
  BigWigURL
[1] "Map Barcodes..."
[1] "Normalize with CPM..."
[1] "LOG: There are 115 intial columns "
[1] "70969845-95d5-4324-ae22-8d8cd725021d"
[2] "c25b7166-f8af-44f2-ae53-e837971dbf37"
[3] "a2885a20-2932-4440-8342-c65d33f73851"
[4] "1fb03f00-e4cd-4750-aabd-d890e7ecbf54"
[5] "71d8638f-6833-4bf8-8f2c-701c8bc59256"
  [1] "TCGA-A6-5664-01A-21R-1839-07" "TCGA-A6-2682-11A-01R-A32Z-07"
  [3] "TCGA-CM-5348-01A-21R-1723-07" "TCGA-A6-2684-01A-01R-1410-07"
  [5] "TCGA-AA-A01C-01A-01R-A00A-07" "TCGA-G4-6314-01A-11R-1723-07"
  [7] "TCGA-F4-6805-01A-11R-1839-07" "TCGA-AZ-6600-01A-11R-1774-07"
  [9] "TCGA-F4-6463-01A-11R-1723-07" "TCGA-AA-A00O-01A-02R-A089-07"
 [11] "TCGA-AA-3968-01A-01R-1022-07" "TCGA-A6-2684-01A-01R-A278-07"
 [13] "TCGA-A6-6781-01B-06R-A277-07" "TCGA-F4-6704-11A-01R-1839-07"
 [15] "TCGA-D5-6922-01A-11R-1928-07" "TCGA-A6-2681-01A-01R-1410-07"
 [17] "TCGA-F4-6704-01A-11R-1839-07" "TCGA-AZ-6607-01A-11R-1839-07"
 [19] "TCGA-G4-6627-01A-11R-1774-07" "TCGA-A6-2684-11A-01R-A32Z-07"
 [21] "TCGA-D5-6924-01A-11R-1928-07" "TCGA-A6-2684-01C-08R-A277-07"
 [23] "TCGA-AA-3520-01A-01R-0821-07" "TCGA-AA-A01K-01A-01R-A00A-07"
 [25] "TCGA-AA-3553-01A-01R-0821-07" "TCGA-A6-A5ZU-01A-11R-A28H-07"
 [27] "TCGA-A6-6782-01A-11R-1839-07" "TCGA-AA-3870-01A-01R-1022-07"
 [29] "TCGA-AA-3860-01A-02R-0905-07" "TCGA-G4-6302-01A-11R-1723-07"
 [31] "TCGA-D5-5538-01A-01R-1653-07" "TCGA-D5-6534-01A-21R-1928-07"
 [33] "TCGA-G4-6310-01A-11R-1723-07" "TCGA-AA-3527-11A-01R-A32Z-07"
 [35] "TCGA-CM-5349-01A-21R-1723-07" "TCGA-A6-3807-01A-01R-1022-07"
 [37] "TCGA-A6-2671-11A-01R-A32Z-07" "TCGA-AZ-6600-11A-01R-1774-07"
 [39] "TCGA-AD-6901-01A-11R-1928-07" "TCGA-A6-2674-01A-02R-A278-07"
 [41] "TCGA-CK-6748-01A-11R-1839-07" "TCGA-A6-2684-01A-01R-1410-07"
 [43] "TCGA-AA-A00D-01A-01R-A002-07" "TCGA-AA-3489-01A-21R-1839-07"
 [45] "TCGA-AD-6899-01A-11R-1928-07" "TCGA-AA-3814-01A-01R-0905-07"
 [47] "TCGA-CM-6169-01A-11R-1653-07" "TCGA-CM-6168-01A-11R-1653-07"
 [49] "TCGA-D5-6929-01A-31R-1928-07" "TCGA-A6-2674-01B-04R-A277-07"
 [51] "TCGA-AA-3538-01A-01R-0821-07" "TCGA-CM-5868-01A-01R-1653-07"
 [53] "TCGA-CM-4752-01A-01R-1410-07" "TCGA-A6-3810-01A-01R-A278-07"
 [55] "TCGA-A6-2671-01A-01R-1410-07" "TCGA-F4-6703-01A-11R-1839-07"
 [57] "TCGA-D5-6926-01A-11R-1928-07" "TCGA-A6-2685-01A-01R-1410-07"
 [59] "TCGA-AD-6964-01A-11R-1928-07" "TCGA-F4-6460-01A-11R-1774-07"
 [61] "TCGA-AA-A00N-01A-02R-A00A-07" "TCGA-AA-3866-01A-01R-1022-07"
 [63] "TCGA-D5-6529-01A-11R-1774-07" "TCGA-A6-3810-01B-04R-A277-07"
 [65] "TCGA-A6-A566-01A-11R-A28H-07" "TCGA-AA-A01D-01A-01R-A00A-07"
 [67] "TCGA-A6-2682-01A-01R-1410-07" "TCGA-A6-6142-01A-11R-1774-07"
 [69] "TCGA-A6-3810-01A-01R-1022-07" "TCGA-A6-2674-01A-02R-0821-07"
 [71] "TCGA-A6-2685-11A-01R-A32Z-07" "TCGA-F4-6809-01A-11R-1839-07"
 [73] "TCGA-F4-6855-01A-11R-1928-07" "TCGA-D5-5541-01A-01R-1653-07"
 [75] "TCGA-A6-2675-11A-01R-1723-07" "TCGA-G4-6297-01A-11R-1723-07"
 [77] "TCGA-AA-3532-01A-01R-0821-07" "TCGA-CK-4948-01B-11R-1653-07"
 [79] "TCGA-A6-6654-01A-21R-1839-07" "TCGA-CM-5341-01A-01R-1410-07"
 [81] "TCGA-AZ-4308-01A-01R-1410-07" "TCGA-CA-6719-01A-11R-1839-07"
 [83] "TCGA-AA-3514-11A-01R-A32Z-07" "TCGA-CM-5860-01A-01R-1653-07"
 [85] "TCGA-CM-5344-01A-21R-1723-07" "TCGA-A6-6781-01A-22R-1928-07"
 [87] "TCGA-CM-6167-01A-11R-1653-07" "TCGA-CM-6679-01A-11R-1839-07"
 [89] "TCGA-AZ-6605-01A-11R-1839-07" "TCGA-AA-3684-01A-02R-0905-07"
 [91] "TCGA-AA-3872-01A-01R-1022-07" "TCGA-F4-6459-01A-11R-1774-07"
 [93] "TCGA-AZ-6605-11A-01R-1839-07" "TCGA-AA-3812-01A-01R-0905-07"
 [95] "TCGA-A6-3808-01A-01R-1022-07" "TCGA-A6-4107-01A-02R-1410-07"
 [97] "TCGA-AA-3514-01A-02R-0821-07" "TCGA-A6-2675-01A-02R-1723-07"
 [99] "TCGA-F4-6807-01A-11R-1839-07" "TCGA-AA-3520-11A-01R-A32Z-07"
[101] "TCGA-D5-6541-01A-11R-1723-07" "TCGA-AA-3489-11A-01R-1839-07"
[103] "TCGA-AA-A00F-01A-01R-A002-07" "TCGA-A6-6781-01A-22R-A278-07"
[105] "TCGA-AA-3527-01A-01R-0821-07" "TCGA-CM-6162-01A-11R-1653-07"
[107] "TCGA-AA-3952-01A-01R-1022-07" "TCGA-D5-6898-01A-11R-1928-07"
[109] "TCGA-A6-2685-01A-01R-1410-07" "TCGA-CM-6165-01A-11R-1653-07"
[111] "TCGA-CA-6717-01A-11R-1839-07" "TCGA-AZ-5403-01A-01R-1653-07"
[113] "TCGA-AA-3867-01A-01R-1022-07" "TCGA-F4-6569-01A-11R-1774-07"
[115] "TCGA-A6-2682-01A-01R-1410-07"
[1] "LOG: There are  mapped columns  "
[1] "LOG: There are 104 non duplicate samples "
[1] "Batch correction for  tcga.gdc_platform"
[1] "LOG: There are 20527 genes that pass mintpm filtering "
[1] "Using logcpm..."
[1] "WARNING: no purity for "
[1] "LOG: There are 104 samples that pass purity filtering "
[1] "Tissue type:  tumor  "
[1] "Get final data..."
[1] "Saving table..."
[1] "LOG: Table dimensions: 20527 x 92 "
[1] "DONE!"
[1] "Saving RDS..."
